Biol 160 Exam III Study Guide

Flashcards covering Lectures 17 to 23 of Biol 160 Exam III, including gene expression regulation, lipid bilayer structure and permeability, cell cycle checkpoints and mitosis, meiosis and genetic diversity mechanisms, and chromosomal abnormalities.

Why do cells regulate gene expression?

Cells regulate gene expression to maintain a balance of resource conservation and rapid response, and to enable differential gene expression so cells can differ depending on their function.

Which level of gene expression regulation is the most energy efficient, and why?

The transcriptional level is the most energy efficient because it stops transcription before it starts.

Which level of gene regulation provides the fastest response according to the lecture notes, and why?

The post-transcriptional level provides the fastest response because there is no folding or modifying of a protein.

What tradeoff exists between transcriptional and post-translational regulation?

The tradeoff between transcriptional and post-translational regulation is energy versus speed.

How does a cell recognize where transcription should begin?

A cell knows where transcription should begin because RNA polymerase recognizes and binds to a specific DNA sequence called a promoter.

What types of information do regulatory DNA sequences provide to transcription machinery?

Regulatory DNA sequences tell transcription machinery where to begin, where to bind, and whether transcription should increase or decrease.

What is a promoter, and where is it located?

A promoter is a DNA sequence where transcription begins, located near the beginning of the gene.

What role do transcription factors play during transcription initiation?

Transcription factors are helper proteins that must arrive first and recruit RNA polymerase.

Is a promoter sequence transcribed into mRNA?

No, a promoter sequence is not transcribed into mRNA.

What are the CAAT and TATA boxes, and what is their function?

The CAAT and TATA boxes are A-T rich sequences that bind transcription factors, which then attract and lock RNA polymerase into place to begin building the RNA strand.

Why are AT-rich regions particularly useful for transcription initiation?

AT-rich sites are useful for transcription initiation because they can be easily broken apart due to having only $2$ hydrogen bonds.

What is an operon, and what components does it include?

An operon is a group of genes in prokaryotes that are controlled together and transcribed as one unit. It includes a promoter, operator, and gene expression.

What is the Lac Operon, and which genes does it contain?

The Lac Operon consists of three genes (lacZ, lacY, lacA) involved in processing the sugar lactose.

What is an enhancer, and how does it influence transcription?

An enhancer is a transcription factor binding site that can be located close to or far from the gene; it increases the rate of transcription.

What is a silencer, and how does it affect transcription?

A silencer is a repressor binding site that down-regulates gene expression, decreasing the rate of transcription via negative regulation.

What is a sigma factor, and what is its role in prokaryotic transcription?

A sigma factor is a protein subunit that helps RNA polymerase find the promoter by attaching directly to RNA polymerase in prokaryotic transcription.

What do eukaryotes use in place of sigma factors for transcription initiation?

Eukaryotes use general transcription factors instead of sigma factors.

What are post-translational modifications?

Post-translational modifications are chemical alterations carried out by enzymes that occur after a protein has been synthesized.

Phosphorylation, glycosylation, and ubiquitination are examples of what regulatory mechanism?

They are examples of post-translational modifications (enzymes that alter a protein).

What are the three main types of lipids in cells, and which type forms biological membranes?

The three main types of lipids in a cell are phospholipids, fats, and steroids. Phospholipids form the cell membrane.

What does it mean that phospholipids are amphipathic?

Phospholipids are amphipathic because they have both hydrophobic (non-polar tail) and hydrophilic (polar head) properties.

What structural feature characterizes steroids such as cholesterol?

Steroids have a four-ring structure and are amphiphilic.

What role does cholesterol play in membrane fluidity, permeability, and stability?

Cholesterol decreases membrane permeability and fluidity, helping maintain membrane stability by preventing it from becoming too fluid or too rigid.

What does selective permeability mean regarding phospholipid bilayers?

Selective permeability means small or nonpolar molecules move across the phospholipid bilayer quickly, whereas charged or large polar substances cross slowly, if at all.

Can phospholipids easily flip from one membrane leaflet to the other? Why or why not?

No, phospholipids cannot flip from one leaflet to another easily because their hydrophobic/hydrophilic structure makes flipping difficult.

What are the major phases of the eukaryotic cell cycle?

The major phases are Interphase (composed of $G_1$, $S$, and $G_2$) and $M$ Phase (Mitosis and Cytokinesis).

What primary molecular events take place during S phase?

During $S$ phase, chromosome replication occurs, DNA is synthesized, and histones are synthesized.

What occurs during the G1 and G2 phases of interphase?

During $G_1$, general cell growth occurs (cells remain or continue based on signals); during $G_2$, tubulin and other proteins necessary for chromosome segregation during mitosis are synthesized.

What is the biochemical function of a kinase, and what does the abbreviation CDK stand for?

A kinase is an enzyme that catalyzes the transfer of a phosphate group from ATP to a target protein (phosphorylation). CDK stands for cyclin-dependent kinase.

How do cyclin levels compare to cyclin-dependent kinase (CDK) levels throughout the cell cycle?

Cyclin levels fluctuate throughout the cell cycle, whereas CDK levels remain constant.

How do cyclins regulate the activity of CDKs to drive cell cycle progression?

Cyclins activate CDKs by functioning like a key; once active, cyclin-CDK complexes phosphorylate downstream components to signal progression through the cell cycle.

What cell parameters are evaluated at the G1 checkpoint?

The $G_1$ checkpoint evaluates cell size, nutrient availability, and DNA damage.

What does the M checkpoint evaluate before allowing chromosome segregation?

The $M$ checkpoint checks whether chromosomes have attached to the spindle apparatus, whether chromosomes have properly segregated, and whether MPF is absent.

What disease condition results from failed cell cycle checkpoints and uncontrolled progression?

Cancer, defined as uncontrollable cell growth that invades other tissues and spreads, where growth-promoting signals remain active when they should be off.

What are the five stages of mitosis in correct sequential order?

Prophase, Prometaphase, Metaphase, Anaphase, and Telophase.

What major structural events occur during prophase and prometaphase of mitosis?

In prophase, chromosomes condense. In prometaphase, the nuclear envelope breaks down and microtubules make contact with kinetochores.

What major events occur during metaphase, anaphase, and telophase of mitosis?

In metaphase, mitotic spindle formation is complete and chromosomes align in the cell center; in anaphase, sister chromatids separate into daughter chromosomes and are pulled apart; in telophase, the nuclear envelope reforms and chromosomes de-condense.

What process immediately follows mitosis to complete cell division, and what molecular mechanism drives it?

Cytokinesis, which is driven by an actin-myosin ring that pinches the plasma membrane until two daughter cells form.

What is the primary biological purpose of mitosis in multicellular organisms?

In multicellular organisms, mitosis functions to replace damaged cells for tissue repair and healing.

What are the ploidy and genetic relationship of daughter cells produced by mitosis relative to parent cells?

Mitosis results in two genetically identical diploid ($2n$) daughter cells.

What are the roles of polar, kinetochore, and astral microtubules during mitosis?

Polar microtubules overlap from opposite poles to push the poles apart; kinetochore microtubules pull chromosomes to the spindle poles; astral microtubules radiate outward from centrosomes to position the spindle apparatus.

What are k-Fibers (kinetochore fibers)?

Kinetochore fibers are bundles of parallel microtubules that connect chromosomes to spindle poles during cell division.

What is the fundamental difference between homologous chromosomes and sister chromatids?

Homologous chromosomes carry different versions of a specific gene called alleles, whereas sister chromatids are two identical copies of a single chromosome.

What is crossing over, and what effect does it have on genetic variation?

Crossing over is the exchange of DNA across homologous chromosomes during Prophase of meiosis, which increases genetic diversity.

What is independent assortment, and how does it generate genetic variability in gametes?

Independent assortment is the process where alleles of two or more genes sort into gametes completely independent of each other, generating genetic variability through numerous combinations.

How does random fertilization amplify genetic variation?

Random fertilization amplifies genetic variation through the random combination of egg and sperm, which yields more than $70\text{ trillion}$ possible zygotes.

What is the fundamental difference in outcomes and separation between Meiosis I and Meiosis II?

Meiosis I separates homologous chromosomes to produce two haploid cells (each chromosome still consist of 2 identical daughter cells)

Meiosis II separates sister chromatids to produce four haploid daughter cells.

Which specific phases of meiosis separate homologous chromosomes and sister chromatids, respectively?

Homologous chromosomes separate during Anaphase I, whereas sister chromatids separate during Anaphase II.

What is the final cellular result of Meiosis II?

The final result is four haploid daughter cells with single, unreplicated chromosomes.

What is ploidy, and how does it differ between human somatic cells and gametes?

Ploidy indicates the number of each type of chromosome. Human somatic cells are diploid ($2n$) with $46$ chromosomes, whereas gametes (sex cells) are haploid ($n$) with $23$ chromosomes.

What is the ploidy level of a zygote?

A zygote is diploid ($2n$).

What is a bivalent?

A bivalent is a pair of homologous chromosomes that have paired up during Prophase of meiosis.

What is a chiasma (chiasmata)?

A chiasma is the $X$-shaped physical point or link where two non-sister chromatids of homologous chromosomes are connected.

What is aneuploidy, and what cellular event causes it?

Aneuploidy is the condition of having too many or too few chromosomes, caused by nondisjunction (when chromosome pairs do not separate properly during cell division).

During which meiotic stages can nondisjunction occur, and how do the gametic outcomes differ?

Nondisjunction can occur during Anaphase I or Anaphase II; nondisjunction in Meiosis I affects all gametes, whereas in Meiosis II it affects half.

Which human genetic syndromes are caused by aneuploidy according to the notes?

Klinefelter Syndrome, Turner Syndrome, and Trisomy 21 (Down's Syndrome).

What maternal factor increases the risk of nondisjunction and Down's syndrome?

Advanced maternal age increases the risk of nondisjunction, especially for Down's syndrome.

Define the four major chromosomal mutations: deletion, inversion, duplication, and translocation.

Deletion: a segment is lost; Inversion: a segment breaks off, reverses direction, and reattaches; Duplication: a segment is copied, resulting in extra genetic material; Translocation: a segment moves to a different location on a nonhomologous chromosome.

What distinguishes balanced (reciprocal) translocation from unbalanced translocation, and what condition can result from translocation between chromosomes 14 and 21?

A balanced translocation is clinically silent (not apparent), whereas an unbalanced translocation is not. A common outcome of translocation involving chromosomes $14$ and $21$ is Down's syndrome.

Given a plasma membrane with hydrocarbons of a set length and temp. We varied the amount of cholesterol.  Which of the following will be most preamble to glycerol

10%

During the G₁ phase, a checkpoint ensures that the cell has sufficient nutrients, appropriate growth signals, and undamaged DNA before proceeding. If a cell has damaged DNA and the G₁ checkpoint fails to stop the cell cycle, what is most likely to occur?

The cell enters S phase with damaged DNA

Based on the results shown in the figure below, which group represents cancer cells?

Group on the right

Somatic cells of a roundworm have 4 chromosomes per cell. How many chromosomes would you expect to find in an ovum (egg) from this roundworm?

2

Which of the following is the inducer of the lac operon?

lactose

Taxol is an anti-breast cancer drug that stops dividing cells at all stages of mitosis. Based on your knowledge of mitosis, which cellular structure is the primary target of Taxol?

microtubules

Which of the following is NOT an example of a post-translational modification of a protein?

Polyadenylation

Which of the following does NOT occur during mitosis?

 

Replication of the DNA

Which of the following are gametes?

 

Sperms and eggs

Kinetochore microtubules (K-fibers) assist in the process of splitting sister chromatids and moving them to the opposite poles by ________.

 

Creating tension by depolymerizing at the kinetochore and pulling the chromatids toward opposite poles

Which of the following best describes how prokaryotic RNA polymerase recognizes a promoter?

 

Sigma factors help RNA polymerase recognize specific promoter sequences

What is the primary function of the Cdk component of MPF?

 

To transfer phosphate groups from ATP to target proteins

The image below shows a cell undergoing anaphase II of meiosis.

false

Compare the roles of promoters, enhancers, silencers, transcription factors, and RNA polymerase in regulating gene expression.

Promoters: upstream of the gene, the binding site of RNA polymerase and transcription factors, A-T rich sequence

Enhancers: transcription factors binding site, can be close or far from gene, increase the rate of transcription

Silencers: repressor binding site to down regulate gene expression, decrease rate of transcription, negative regulation

Transcription Factors: attract an lock in RNA polymerase

RNA Polymerase: synthesizes the single stranded RNA

What are the post translational chemical modifications of target protein?

Phosphorylation

Glycosylation

Ubiquitination

Acetylation

Methylation